Variant report

Variant	rs1569199
Chromosome Location	chr10:54079716-54079717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
2	chr10:54077756..54080731-chr10:54080779..54082733,3	MCF-7	breast:
3	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:
4	chr10:54068768..54071357-chr10:54075695..54080723,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231131	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11001560	0.80[EUR][1000 genomes]
rs11001584	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11815201	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1528877	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1569198	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7087520	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv895400	chr10:54073294-54094359	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1569199	PRKG1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54077600-54080600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr10:54077800-54080600	Enhancers	HSMMtube	muscle
3	chr10:54078200-54080000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:54078200-54080400	Enhancers	Osteobl	bone
5	chr10:54078400-54080000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:54078400-54080400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:54078400-54080400	Enhancers	Hela-S3	cervix
8	chr10:54078400-54080400	Enhancers	NH-A	brain
9	chr10:54078400-54080600	Enhancers	HMEC	breast
10	chr10:54078400-54080600	Genic enhancers	HSMM	muscle
11	chr10:54078400-54080600	Enhancers	NHEK	skin
12	chr10:54078400-54094800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:54078600-54080600	Enhancers	NHDF-Ad	bronchial
14	chr10:54078600-54082200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr10:54078600-54093200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:54078800-54080000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:54078800-54080400	Enhancers	NHLF	lung
18	chr10:54078800-54080600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr10:54078800-54080800	Enhancers	HUVEC	blood vessel
20	chr10:54079000-54080000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr10:54079200-54079800	Flanking Active TSS	A549	lung
22	chr10:54079600-54080200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:54079600-54080200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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